Standard & Custom Analysis

Standard Analysis

Files provided with different standard analyses at McDermott center Bioinformatics Lab:

RNA sequencing

  1. Raw unprocessed gzipped FASTQ files
  2. FASTQC report with basic sequencing quality statistics
  3. Mapped BAM files (bam format)
  4. Alignment report
  5. Normalized bigwig files (coverage files)
  6. Clustering, dendrogram, report
  7. MDS plot, MA plot, Volcano plot
  8. EdgeR output differential expression files

ChiP Sequencing

  1. Raw unprocessed gzipped FASTQ files
  2. FASTQC report with basic sequencing quality statistics
  3. Mapped BAM files
  4. Normalized wiggle and bigwig files
  5. ChIP-Seq quality measures (phantompeakqualtools)
  6. HOMER-generated analysis output files
  7. MACS2 generated peak files
  8. Peak annotated files

Exome Sequencing

  1. Raw unprocessed gzipped FASTQ files
  2. FASTQC report with basic sequencing quality statistics
  3. Mapped BAM files
  4. Mapping statistics
  5. PICARD metrics
  6. Coverage statistics (plots, target region coverage, mean coverage, etc.)
  7. Annotated Variant calls in VCF formats and tab-delimited format

Custom Analysis

Other than the free data analysis provided by the McDermott Bioinformatics Lab, we can also tailor pipelines based on project needs. The expectations and analysis requirements need to be discussed in detail with us before a quote can be made. For example, the following scenarios could be characterized as "Custom Analysis":

  • Mapping to a custom genome
  • Using software not part of the McDermott Bioinformatics pipeline
  • Data not generated by the McDermott Sequencing Core
  • If the data needs to be re-analyzed for reasons such as tweaking software parameters, using extra data in the analysis
  • Analyses not based on general bioinformatics such as RNA-Seq, ChIP-Seq, Whole Exome/Whole Genome sequencing, Amplicon sequencing, Gro-Seq, SmallRNA, Cancer-related.
  • Generate publication-ready charts and figures. For example heatmaps volcano plots, hierarchical clustering

For more specific scenarios please view the following. We have the knowledge and means of providing far more detailed analysis that needs manual intervention not achievable through our automated pipeline. The following is intended to give you some idea of the detailed analysis we can provide.

Exon Capture/Whole Genome

  • Pedigree-based analysis

ChiPSeq

  • Further filtering of enriched genesets based on project specific criteria
  • Intersection/Union of peaks between different conditions
  • IP analysis
  • Pathway analysis (such as IPA)

RNA-Seq

  • Use alternate combinations of samples/groups for differential expression analysis other than the ones initially requested
  • Intersection/union of genesets between samples/groups
  • Further filtering of enriched genesets based of project specific criteria
  • Pathway analysis (such as IPA)
  • Xenograft